Search publications
19 results for “Guide”
-
Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.
Nature chemical biology · 2025
Endogenous uridine-rich small nuclear RNAs (U snRNAs) form RNA-protein complexes to process eukaryotic pre-mRNA into mRNA. Previous studies have demonstrated programmable U snRNA guide-targeted exon inclusion and exclusion. Here we investigated whether snRNAs can also enhance RNA base editing over …
PMID 40968292 DOI ↗
-
Strategies for programmable manipulation of alternative splicing.
Current opinion in genetics & development · 2024 · 89: 102272
Alternative splicing (AS) plays a pivotal role in protein diversity and mRNA maturation. Programmable control of targeted AS events is of longstanding interest in RNA biology, promising correction of dysregulated splicing in disease and discovery of AS events. This review …
PMID 39471777 DOI ↗
-
Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts.
bioRxiv : the preprint server for biology · 2024
Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can …
PMID 38915553 DOI ↗
-
Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans.
Nature medicine · 2022 · 28(7): 1372-1376
RNA-guided RNA-targeting nucleases, such as CRISPR-Cas13 proteins, have therapeutic potential for gene editing. Among Cas13d enzymes, Cas13d from the bacteria Ruminococcus flavefaciens (RfxCas13d) is of particular interest owing to its small size and high specificity. However, the existence of pre-existing …
PMID 35668177 DOI ↗
-
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.
Nature protocols · 2022 · 17(5): 1223-1265
Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which …
PMID 35322209 DOI ↗
-
Crosstalk between CRISPR-Cas9 and the human transcriptome.
Nature communications · 2022 · 13(1): 1125
CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 …
PMID 35236841 DOI ↗
-
A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation.
Blood advances · 2021 · 5(5): 1310-1323
The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and is disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined central role, and mutations promote malignant transformation. More …
PMID 33656539 DOI ↗
-
The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1.
Nature biomedical engineering · 2021 · 5(2): 157-168
Myotonic dystrophy type I (DM1) is a multisystemic autosomal-dominant inherited human disorder that is caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of DMPK. Toxic RNAs expressed from such repetitive sequences can be eliminated using CRISPR-mediated …
PMID 32929188 DOI ↗
-
The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism.
RNA (New York, N.Y.) · 2020 · 26(11): 1557-1574
RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate …
PMID 32669294 DOI ↗
-
Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing.
Cell reports · 2020 · 33(5): 108350
Site-directed RNA editing approaches offer great potential to correct genetic mutations in somatic cells while avoiding permanent off-target genomic edits. Nuclease-dead RNA-targeting CRISPR-Cas systems recruit functional effectors to RNA molecules in a programmable fashion. Here, we demonstrate a Streptococcus pyogenes …
PMID 33147453 DOI ↗
-
Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.
Nature methods · 2020 · 17(6): 636-642
Genetic screens using pooled CRISPR-based approaches are scalable and inexpensive, but restricted to standard readouts, including survival, proliferation and sortable markers. However, many biologically relevant cell states involve cellular and subcellular changes that are only accessible by microscopic visualization, and …
PMID 32393832 DOI ↗
-
RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering.
Nature cell biology · 2020 · 22(2): 143-150
Deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and parallel systems is further explored, RNA manipulation is emerging as a powerful mode of CRISPR-based engineering. In this Perspective, …
PMID 32015437 DOI ↗
-
Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels.
Molecular cell · 2018 · 69(6): 1005-1016.e7
RNA binding proteins (RBPs) interact with primary, precursor, and mature microRNAs (miRs) to influence mature miR levels, which in turn affect critical aspects of human development and disease. To understand how RBPs contribute to miR biogenesis, we analyzed human enhanced …
PMID 29547715 DOI ↗
-
Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells.
Nature · 2016 · 532(7600): 508-511
Umbilical cord blood-derived haematopoietic stem cells (HSCs) are essential for many life-saving regenerative therapies. However, despite their advantages for transplantation, their clinical use is restricted because HSCs in cord blood are found only in small numbers. Small molecules that enhance …
PMID 27121842 DOI ↗
-
A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions.
Cell · 2016 · 165(2): 396-409
Multiple division cycles without growth are a characteristic feature of early embryogenesis. The female germline loads proteins and RNAs into oocytes to support these divisions, which lack many quality control mechanisms operating in somatic cells undergoing growth. Here, we describe …
PMID 27020753 DOI ↗
-
Applications of Cas9 as an RNA-programmed RNA-binding protein.
BioEssays : news and reviews in molecular, cellular and developmental biology · 2015 · 37(7): 732-9
The Streptococcus pyogenes CRISPR-Cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the Cas9 protein and guide RNAs enables recognition of specific DNA sequences. The recent discovery that Cas9 can …
PMID 25880497 DOI ↗
-
Comprehensive identification of miRNA target sites in live animals.
Methods in molecular biology (Clifton, N.J.) · 2011 · 732: 169-85
MicroRNAs (miRNAs) are small RNA molecules that posttranscriptionally regulate the expression of protein-coding genes. The mature miRNAs are loaded into Argonaute-containing protein complexes (miRISC, miRNA Induced S ilencing Complex), and guide these complexes to the 3' UTR of targeted mRNA …
PMID 21431713 DOI ↗
-
Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans.
Nature structural & molecular biology · 2010 · 17(2): 173-9
MicroRNAs (miRNAs) regulate gene expression by guiding Argonaute proteins to specific target mRNA sequences. Identification of bona fide miRNA target sites in animals is challenging because of uncertainties regarding the base-pairing requirements between miRNA and target as well as the …
PMID 20062054 DOI ↗
-
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model.
Proceedings of the National Academy of Sciences of the United States of America · 2008 · 105(51): 20179-84
High-throughput sequencing has rapidly gained popularity for transcriptome analysis in mammalian cells because of its ability to generate digital and quantitative information on annotated genes and to detect transcripts and mRNA isoforms. Here, we described a double-random priming method for …
PMID 19088194 DOI ↗
Datasets 10
Investigating m6A-relevant gene function in neural progenitor cells using CRISPR-Cas9 genome editing and RNA-seq
Homo sapiens · GPL24676
Next Generation Sequencing: in vivo genome-wide CRISPR sgRNA screen in primary cancer-initiating and propagating bcCML stem cells
Mus musculus · GPL21103
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Homo sapiens · GPL15520
CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production
Homo sapiens · GPL20301
Crosstalk between CRISPR-Cas9 and the human transcriptome
Homo sapiens · GPL20301
Microsatellite expansion RNA visualization, elimination, and reversal of molecular pathology by RNA-targeting Cas9
Homo sapiens · GPL20301
A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions
6239 · GPL18245
The Thermus thermophilus DEAD-box protein Hera is a general RNA chaperone and plays a key role in tRNA metabolism
Thermus thermophilus HB27 · GPL27012
Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs
Homo sapiens · GPL34284
Analyses 0
No analyses match this query.